Basic Data Visualization

Differentially Expressed Genes

Example 1

STRING Network Up-regulated genes:

STRING Network Downregulated Genes:

STRING Enrichment Analysis Piecharts:

Example 2

Visualisation of Ovarian Cancer Network:

Visualisation of Ovarian Cancer Drivers:

Connecting to RCys3

if (!requireNamespace("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("RCy3")
library(RCy3)
cytoscapePing()
 cytoscapeVersionInfo ()

#4 My first network

nodes <- data.frame(id=c("node 0","node 1","node 2","node 3"),
           group=c("A","A","B","B"), # categorical strings
           score=as.integer(c(20,10,15,5)), # integers
           stringsAsFactors=FALSE)
edges <- data.frame(source=c("node 0","node 0","node 0","node 2"),
           target=c("node 1","node 2","node 3","node 3"),
           interaction=c("inhibits","interacts","activates","interacts"),  # optional
           weight=c(5.1,3.0,5.2,9.9), # numeric
           stringsAsFactors=FALSE)

createNetworkFromDataFrames(nodes,edges, title="my first network", collection="DataFrame Example")
setVisualStyle('Marquee')

style.name = "myStyle"
defaults <- list(NODE_SHAPE="diamond",
                 NODE_SIZE=30,
                 EDGE_TRANSPARENCY=120,
                 NODE_LABEL_POSITION="W,E,c,0.00,0.00")
nodeLabels <- mapVisualProperty('node label','id','p')
nodeFills <- mapVisualProperty('node fill color','group','d',c("A","B"), c("#FF9900","#66AAAA"))
arrowShapes <- mapVisualProperty('Edge Target Arrow Shape','interaction','d',c("activates","inhibits","interacts"),c("Arrow","T","None"))
edgeWidth <- mapVisualProperty('edge width','weight','p')

createVisualStyle(style.name, defaults, list(nodeLabels,nodeFills,arrowShapes,edgeWidth))
setVisualStyle(style.name)

lockNodeDimensions(FALSE, style.name)

#5 Bioconductor graph example

g = new ('graphNEL', edgemode='directed')
    g = graph::addNode ('A', g)
    g = graph::addNode ('D', g)
    g = graph::addNode ('C', g, edges = list('D'))
    g = graph::addNode ('B', g, edges = list(c('A','D','C')))
    createNetworkFromGraph (g, title='simple network', collection='GraphNEL Example')

 df <- data.frame (moleculeType=c('kinase','TF','cytokine','cytokine'),
                     log2fc=c(1.8,3.0,-1.2,-2.5),
                     row.names = c('A','B','C','D'), # row.names = node names
                     stringsAsFactors = FALSE)       # important when loading strings!
    loadTableData (df)
setNodeShapeDefault ('OCTAGON')
    setNodeColorDefault ('#AAFF88')
    setNodeSizeDefault  (60)
    setNodeFontSizeDefault (30)

getNodeShapes ()   # diamond, ellipse, trapezoid, triangle, etc.
    column <- 'moleculeType'
    values <- c ('kinase',  'TF','cytokine')
    shapes <- c ('DIAMOND', 'TRIANGLE', 'RECTANGLE')
    setNodeShapeMapping (column, values, shapes)

column <- 'log2fc'
    control.points <- c (-3.0, 0.0, 3.0)
    colors <-  c ('#5588DD', '#FFFFFF', '#DD8855')
    setNodeColorMapping (column, control.points, colors)

control.points <- c (-2.0, 0.0, 2.0)
    colors <-  c ('#2255CC', '#5588DD', '#FFFFFF', '#DD8855','#CC5522')
    setNodeColorMapping (column, control.points, colors)

 control.points = c (-3.0, 2.0, 3.0)
    sizes     = c (20, 80, 90)
    setNodeSizeMapping (column, control.points, sizes)
    selectNodes ('C','name')
 getSelectedNodes ()
    selectFirstNeighbors ()
saveSession('vignette_session') #.cys
full.path=paste(getwd(),'vignette_image',sep='/')
    exportImage(full.path, 'PNG', zoom=200) #.png scaled by 200%
    exportImage(full.path, 'PDF') #.pdf
    ?exportImage

#6 Browse available functions, commands and arguments

help(package=RCy3)
cyrestAPI()  # CyREST API
commandsAPI()  # Commands API
commandsHelp("help")  
commandsHelp("help network")  
commandsHelp("help network select") 
browseVignettes("RCy3")